nickReference: Mapping nick label location from contig to reference

In VilainLab/methometR: methometR: Extracting methylation information from Optical Genome Maps

Description

Mapping nick label location from contig to reference

Usage

nickReference(
  refxmap,
  refcmap,
  contigcmap,
  contigID,
  returnMethod = c("Text", "dataFrame"),
  hmdir,
  chrom
)

Arguments

refxmap	character. contig reference xmap data.
refcmap	character. reference cmap data.
contigcmap	character. contig cmap data.
contigID	character. query contig ID.
returnMethod	character. Output method. Text or dataframe.
hmdir	integer. Home Directory.
chrom	integer. chromosome number.

Value

dataframe containing the molecule file, with the reference position

Examples

refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
refCmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/hg19ref_r.cmap", package="methometR")
Contigqcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/SampContig_q.cmap", package="methometR")
refxmapdat <- readingXmap(refcontigXmap)
refcmapdat <- readingCmap(refCmap)
contigcmapdat <- readingCmap(Contigqcmap)
nickRef<-nickReference(refxmap = refxmapdat, refcmap = refcmapdat, 
    contigcmap = contigcmapdat, contigID = 6701, 
   returnMethod =c("dataFrame"),  chrom = 4)

VilainLab/methometR documentation built on Dec. 18, 2021, 6:17 p.m.